Auto Paper

Use this as the auto-paper orchestrator, not a polishing tool. It routes phases and checks artifacts without inventing paper state.

Boundaries

• Author evidence outranks exemplars: local results, figures, tables, notes, approved claim boundaries, and operator facts.
• Do not invent experiments, results, mechanisms, statistics, novelty, clinical meaning, data availability, citations, or source support.
• Blogs, reviews, surveys, and tutorials are citation-supported by default unless the operator explicitly asks for an uncited opinion memo.
• External papers are examples for structure, style, terminology, and positioning, not author claims.
• Patch LaTeX only from written artifacts.
• Read experiment results primarily through docs/30_evidence/Experiment_Evidence_Index.{json,md} and artifact paths named there. Direct iteration_log.json reads are weak intent signals; paper claims require reports, configs, logs, metrics, or run artifacts.
• Read docs/context/experiments.md when present for Research Wiki context, stable observations, run requests, assurance gaps, and open questions. Legacy docs/45_discoveries/Research_Wiki.md is a fallback before dynamic-context-v2 migration; neither file is approval.
• Do not write iteration_log.json, .auto_iterate/**, or hidden controller state. Durable paper artifacts live under auto_paper_output/<paper_id>/.

Required Config

Before the loop, establish paper_id, workflow, venue/target, draft path, TeX roots, bibliography paths, figures, materials, references, artifact dir, optional experiment evidence index, output language, citation target count, figure/table requirement status, compile command, human gate policy, and forbidden directions in auto_paper_output/<paper_id>/config.yaml or an intake artifact. If missing, route to $auto-paper-intake or return USER_GATE.

After Grill establishes an Automation Policy, paper phases auto-proceed within that policy. Use USER_GATE only for missing operator intent, explicit approval tools, or irreversible external submit.

Use the deterministic checker when the operator requests an automatic paper chain:

python tooling/auto_paper/scripts/auto_paper/artifact_check.py \
  auto_paper_output/<paper_id> --phase <phase> --json

The checker reports artifact readiness only; it does not invent manuscript content or prove scientific claims.

Phase Route

Run in order unless an audit routes back: $auto-paper-research, $auto-paper-argument, $auto-paper-citation, $auto-paper-layout, $auto-paper-patch, $auto-paper-harden.

Optional branches: $auto-paper-response, $auto-paper-data, $auto-paper-figure. Enter $auto-paper-figure when the operator asks for figure work, TeX or source files mention needed figures/tables, or harden finds figure/caption risk.

Artifacts

Durable decisions live under auto_paper_output/<paper_id>/.

• Intake: config.yaml, source_index.md, tex_inventory.json, intake_report.md, experiment_source_map.md, optional figure_requirement_scan.md
• Phase artifacts: research dossier, style/gap maps, confirmed motivation, claim register, citation support bank, section blueprints, rationale matrix, citation and patch plans, figure contracts, patch ledgers, audits, and final gate ledger
• run_request_register.{json,md} when missing experiments are needed

Use references/artifact-contract.md for identifiers and stale-artifact policy.

Gate And Routing

Do not patch around missing upstream artifacts. Every audit finding names root_cause, owning_phase, required_artifact, fix_action, and downstream_risk.

Decisions: NEXT_UNIT, REWORK_RESEARCH, REWORK_ARGUMENT, REWORK_CITATION, REWORK_LAYOUT, REWORK_PATCH, RUN_REQUEST, USER_GATE, COMPLETE, ABORT.

RUN_REQUEST means writing found missing experiment evidence for $run. Record the blocking claim, needed evidence, minimum artifacts, suggested prompt, and acceptance check in run_request_register.{json,md}.

When a draft introduces, narrows, or removes a result claim, record Claim Delta Evidence in the phase artifact or Gate ledger. Unsupported claims become RUN_REQUEST, not a default approval pause.

References

Load only active-phase references from references/: loop, auto-iterate boundary, artifact contract, writing rationale, motivation thread, citation support, and LaTeX source control.

Use deterministic helpers when available:

• .agents/skills/auto-paper/scripts/figure_requirement_scan.py
• ../../../.agents/references/research-supervision-patterns.md
• ../../../.agents/references/research-supervision/README.md

Output

Final responses report artifact manifest, modified files, guard/compile results, remaining reviewer risks, and next human gates.